In eukaryotes, most of the genes are found in the nucleus, but genes are also present in plastids and chloroplasts.

Genes are shuffled in every generation of sexually reproducing organisms via meiosis and fertilization.

4Genomes and Their Evolution

For a gene to be passed on to successive generations, the individual with that gene must survive and reproduce.

A genes capacity to cooperate with different combinations of other genes will likely increase its probability of transmission.

The genes of an individual can be viewed as interacting members of a group in which there are divisions of labor and strong interdependencies.

5Genomes and Their Evolution

Studies of genomic evolution look at the genome of an organism as an integrated whole and attempt to answer questions such as

How do proteins acquire new functions?

Why are the genomes of different organisms so variable in size?

How has the enlargement of genomes been accomplished?

6The Evolution of Macromolecules

The molecules of interest to molecular evolutionists are nucleotides, nucleic acids, amino acids, and proteins.

Molecular evolutionists investigate the evolution of these macromolecules to determine how rapidly they change and why they have changed.

Knowledge of the rate of change of a given macromolecule is crucial to attempts to reconstruct the evolutionary history of groups of organisms.

7The Evolution of Macromolecules

Nucleic acids evolve when nucleotide base substitutions occur.

Substitutions can change the amino acid sequence, and thus the structure and function, of the polypeptides.

By characterizing nucleic acid sequences and the primary structures of proteins, molecular evolutionists can determine how rapidly these macromolecules have changed and why they changed.

8The Evolution of Macromolecules

Molecular evolution differs from phenotypic evolution in one important way In addition to natural selection, random genetic drift and mutation exert important influences on the rates and directions of molecular evolution.

A mutation is any change in the genetic material.

9The Evolution of Macromolecules

Many mutations, called silent or synonymous mutations, do not alter the proteins they encode.

This is because most amino acids are specified by more than one codon in the universal genetic code.

For example, leucine is specified by six different codons UUA, UUG, CUU, CUC, CUA, and CUG.

Since silent mutations are unlikely to be influenced by natural selection, they are free to accumulate in a population over time at rates determined by rates of mutation and genetic drift.

10The Evolution of Macromolecules

A nonsynonymous mutation does change the amino acid sequence.

For example, UUA to UUC would result in a phenylalanine rather than a leucine in the protein.

Nonsynonymous mutations are usually deleterious, but those that dont alter the proteins shape may be selectively neutral.

Most natural populations of organisms harbor much more genetic variation than would be expected if genetic variation were influenced primarily by natural selection.

11Figure 26.1 When One Base Does or Doesnt Make a Difference 12The Evolution of Macromolecules

The neutral theory postulates that, at the molecular level, the majority of mutations are selectively neutral.

If so, the majority of evolutionary changes in macromolecules, and much of the genetic variation within species, result from neither positive selection of advantageous alleles nor stabilizing selection, but from random genetic drift.

13The Evolution of Macromolecules

Using the rationale that the rate of fixation of mutation is theoretically constant and equal to the neutral mutation rate, the concept of the molecular clock was developed.

The concept of the molecular clock states that macromolecules should diverge from one another at a constant rate.

14Determining and Comparing theStructure of Macromolecules

Biologists must determine the precise structure of macromolecules to investigate patterns of molecular evolution.

PCR allows biologists to amplify ancient DNA to concentrations that can be used in experiments to determine its sequence.

When the amino acid sequences of proteins from different organisms have been determined, they can be compared by sequence alignment.

The much slower rate of mutation at sites that do affect molecular function is consistent with the view that most nonsynonymous mutations are disadvantageous and are eliminated from the population by natural selection.

In general, the more essential a molecule is for cell function, the slower the rates of its evolution.

A molecule that illustrates this principle is the enzyme cytochrome c, a component of the respiratory chain in mitochondria.

Some of the apparent differences in genome size disappear when the portion of DNA that actually codes for RNA or protein is compared.

The size of the coding genome varies in a way that makes sense

Eukaryotes have more coding DNA than prokaryotes.

Plants have more than single-celled organisms.

Vertebrates have more than nonvertebrates.

33The Evolution of Genome Size

Most of the variation in genome size is due to the amount of noncoding DNA an organism has.

Much of the noncoding DNA may consist of pseudogenes that are carried with the genome because the cost of doing so is small.

Some of the DNA consists of transposable elements that spread through populations because they reproduce faster than the host genome.

34Figure 26.8 A Large Proportion of DNA Is Noncoding 35The Evolution of Genome Size

Retrotransposons are being used by scientists to determine the rates at which species lose DNA.

The most common type carries long terminal repeats (LTRs) at each end.

Occasionally, LTRs join together in the host genome, causing the DNA between them to be excised and leaving one of the LTRs behind.

The number of these orphaned LTRs in a genome is a measure of how many retrotransposons have been lost.

Scientists can use the number of LTRs present in the genomes of different organisms to compare their rates of DNA loss.

36The Evolution of Genome Size

Two identical copies of a gene can have one of three different fates

Both copies may retain their original function.

One copy may become incapacitated by the accumulation of deleterious mutations and become a pseudogene.

One copy may retain its original function while the other accumulates enough mutations that it can perform a different function.

The third is the most significant for evolution.

37The Evolution of Genome Size

The frequency of gene duplications and their outcome can be assessed by counting the number of synonymous nucleotide base changes in the genome and then comparing that with the number of base changes causing protein alterations.

The rates of gene duplication are fast enough for a yeast or Drosophila population to acquire several hundred duplicate genes over the course of a million years.

Although most duplicate genes disappear rapidly on an evolutionary time scale, some duplications lead to the evolution of genes with new functions.

38The Evolution of Genome Size

Several rounds of duplication and mutation may lead to formation of a gene family, a group of homologous genes with related functions.

There is evidence that the globin gene family arose by gene duplication.

To estimate the time of the first globin gene duplication, a gene tree can be created.

Based on the gene tree, the two globin gene clusters are estimated to have split about 450 mya.

Understanding the genomes of pathogens and the organisms that carry them has already had medical benefits.

The determination of the genomes of Anopheles and Plasmodium has allowed scientists do develop transgenic mosquitoes that express an anti-Plasmodium molecule that makes them inefficient vectors of malaria in the lab.

Information provided by the genomic sequence of Treponema pallidum, the bacterium that causes syphilis, is being used to develop a vaccine against this disease.

45The Uses of Molecular Genomic Information

The AIDS epidemic reminds us that molecular data, while providing powerful tools in our struggle with diseases, cannot solve all medical problems.

A highly active antiretroviral therapy (HAART) is generally used to treat AIDS patients.

Unfortunately, strains of resistant HIV develop in the blood of most patients that receive HAART.

The combination of a high mutation rate and no repair mechanism means that a new mutant is generated every time HIV replicates its genome.

46The Uses of Molecular Genomic Information

Scientific understanding of the evolutionary patterns of life on Earth and how the agents of evolution governed those patterns is advancing more rapidly than ever.

By combining molecular data with information from the fossil record, biologists are developing an increasingly comprehensive picture of the evolution of life on Earth.

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